Patterson and Hennessy is a clear and frequently-used textbook for computer architecture, appropriate for a graduate core course. This book concentrates on the best way to design a computer, particularly the main instruction pipeline, in general. Beware: it won't be much help in understanding how your specific machine works, particularly its peripherals (e.g. the protocol for communicating with your graphics card). Also, it is expensive.
Messmer is an excellent reference for PC hardware, both the main processor and peripherals. Clear, comprehensive, detailed, and assumes little background in hardware. Ferraro is a readable and comprehensive reference for standard graphics cards found on PC's.
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PC Magazine covers the entire range of products, but is badly edited. The other two magazines are more specialized, but well written.